apiVersion: batch/v1
kind: Job
metadata:
  name: nf-fc2022e37a458178aab194efa43a5ffc-95e53
  namespace: nextflow
  labels: &id001 {nextflow.io/processName: NFCORE_SAREK_SAREK_BAM_VARIANT_CALLING_SOMATIC_ALL_BAM_ESTIMATE,
    nextflow.io/runName: mimsi-altera-exact-specimens-20260604-225411, nextflow.io/sessionId: uuid-dd28c81f-e91d-434d-b2df-f796b65d8ca1,
    pltf/run-name: mimsi-altera-exact-specimens-20260604-225411, capacityType: spot,
    pltf/run-component: task, nextflow.io/app: nextflow, nextflow.io/taskName: NFCORE_SAREK_SAREK_BAM_VARIANT_CALLING_SOMATIC_ALL_BAM_ESTIMATE,
    pltf/run-id: 6cb5a227, pltf/run-engine: nextflow, instanceLocalNvme: 'false',
    pltf/run-creator: mbotlaniesfahani}
  annotations: &id002 {ad.datadoghq.com/nextflow.logs: '[{"source":"nextflow","service":"nextflow-task","log_processing_rules":[{"type":"multi_line","name":"nextflow_task_multiline","pattern":"^\\x00NEVER_MATCH"}]}]',
    ad.datadoghq.com/tags: '{"run_name":"mimsi-altera-exact-specimens-20260604-225411","run_id":"6cb5a227","run_creator":"mbotlaniesfahani","run_component":"task","task_process":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_ESTIMATE_SEX_NORMAL","task_name":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_ESTIMATE_SEX_NORMAL
      (1173_H2E-N1-BDNA-01_B23MHTGLT4_1)"}', karpenter.sh/do-not-disrupt: 'true'}
  ownerReferences:
  - {apiVersion: v1, kind: Pod, name: mimsi-altera-exact-specimens-20260604-225411-6cb5a227-vf9d8,
    uid: 2bc27940-dac2-46ae-ac72-b9b8fdb8fabb, controller: true, blockOwnerDeletion: true}
spec:
  backoffLimit: 0
  template:
    metadata:
      name: nf-fc2022e37a458178aab194efa43a5ffc-95e53
      namespace: nextflow
      labels: *id001
      annotations: *id002
    spec:
      restartPolicy: Never
      containers:
      - name: nextflow
        image: 292967571998.dkr.ecr.us-west-2.amazonaws.com/quay/biocontainers/samtools:1.21--h50ea8bc_0
        args: [/bin/bash, -o, pipefail, -c, 'trap "{ ret=$?; /opt/s5cmd/bin/s5cmd
            --log error cp .command.log s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/2022e37a458178aab194efa43a5ffc/.command.log||true;
            exit $ret; }" EXIT; /opt/s5cmd/bin/s5cmd --log error cat s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/2022e37a458178aab194efa43a5ffc/.command.run
            | bash 2>&1 | tee .command.log']
        workingDir: /tmp
        imagePullPolicy: Always
        env:
        - {name: SSL_CERT_FILE, value: /opt/s5cmd/ssl/ca-certificates.crt}
        - {name: SSL_CERT_DIR, value: /opt/s5cmd/ssl/certs}
        resources:
          requests: {cpu: 1, memory: 4096Mi, ephemeral-storage: 204800Mi}
          limits: {memory: 4096Mi, ephemeral-storage: 204800Mi}
        volumeMounts:
        - {name: vol-1225, mountPath: /app}
        - {name: vol-1226, mountPath: /tmp}
        - {name: vol-1227, mountPath: /mnt/secrets}
        - {name: vol-1228, mountPath: /opt/s5cmd}
      nodeSelector: {workload: nextflow-task, karpenter.sh/capacity-type: spot}
      affinity:
        nodeAffinity:
          requiredDuringSchedulingIgnoredDuringExecution:
            nodeSelectorTerms:
            - matchExpressions:
              - {key: eks.amazonaws.com/instance-gpu-count, operator: DoesNotExist}
      serviceAccountName: sa-nextflow
      securityContext: {runAsUser: 1000}
      tolerations:
      - {key: workload, operator: Equal, value: nextflow-task, effect: NoSchedule}
      activeDeadlineSeconds: 14400
      volumes:
      - name: vol-1225
        emptyDir: []
      - name: vol-1226
        emptyDir: []
      - name: vol-1227
        secret: {secretName: aws-secrets-manager}
      - name: vol-1228
        hostPath: {path: /opt/s5cmd}
  ttlSecondsAfterFinished: 28800